MRC Laboratory of Molecular Biology

The assembly of tau into amyloid filaments is associated with more than 20 neurodegenerative diseases, collectively termed tauopathies. Electron cryo-microscopy (cryo-EM) structures of brain-derived tau filaments revealed that specific structures define different diseases, triggering a quest for the development of experimental model systems that replicate the structures of disease. Here, we describe 12 phosphomimetic serine/threonine-to-aspartate mutations in tau, which we term PAD12, that collectively induce the in vitro assembly of full-length three-repeat tau into filaments with the same structure as paired helical filaments extracted from the brains of individuals with Alzheimer's disease. Solution-state nuclear magnetic resonance spectroscopy suggests that phosphomimetic mutations in the carboxy-terminal domain of tau may facilitate filament formation by disrupting an intramolecular interaction between two IVYK motifs. PAD12 tau can be used for both nucleation-dependent and multiple rounds of seeded assembly in vitro, as well as for the seeding of tau biosensor cells. PAD12 tau can be assembled into paired helical filaments under various shaking conditions, with the resulting filaments being stable for extended periods of time. They can be labelled with fluorophores and biotin. Tau filaments extracted from the brains of individuals with Alzheimer's disease have been known to be made of hyperphosphorylated and abnormally phosphorylated full-length tau, but it was not known if the presence of this post-translational modification is more than a mere correlation. Our findings suggest that hyperphosphorylation of tau may be sufficient for the formation of the Alzheimer tau fold. PAD12 tau will be a useful tool for the study of molecular mechanisms of neurodegeneration.

Abstract The Trimethyl guanosine Synthase (TGS1) is a highly conserved enzyme mediating di-methylation of the 5’-cap 7-methylguanosine of RNA to generate 2,2,7-trimethylguanosine (m 2,2,7 G). Known TGS1 targets include snRNAs, snoRNAs, the telomeric RNA component and a limited number of mRNAs encoding selenoproteins. TGS1 is highly expressed in acute myeloid leukaemia (AML) cells, and its expression correlates with poor prognosis. Here, we report that TGS1 directly methylates the cap of more than 500 mRNAs in AML cells. Specifically, we demonstrate that TGS1 modifies nuclear mRNAs encoding mitochondrial proteins, including critical components of complexes involved in both the TCA cycle and oxidative phosphorylation, promoting their translation mediated by mitochondria associated cytosolic ribosomes. Functionally, we report that TGS1 depletion impairs mitochondrial respiration and increases oxidative stress. This, in turn, impairs the growth of AML cells causing differentiation and cell cycle arrest in vitro and in vivo . Finally, we demonstrate that TGS1 depletion sensitizes AML cells to RSL3, a small molecule promoting ferroptosis. Taken together, our findings establish TGS1 as a key regulator of oxidative phosphorylation and mitochondrial redox status of AML cells and highlight its potential as a therapeutic target in leukaemia.

ABSTRACT During development, the size of the neuroepithelial cell pool plays a key role in establishing brain size, determining the numbers of derived progenitors and subsequent neuronal cell types. While early histogenesis is well modelled in brain organoids, the organ-scale geometry of the telencephalon is not accurately recapitulated. Herein, we present a new approach for generating ventral and dorsal forebrain organoids which develop a large ventricular neuroepithelium, characteristic of the closed telencephalic vesicle. Using a growth medium that supports aerobic glycolysis and is typically used for endothelial cells, we modulate neuroepithelial expansion to induce a more anatomically accurate neuroepithelial layer which, upon maturation, thickens physiologically to generate the typical neurogenic layered architecture. In addition, we present a new method for embedding organoids in miniature collagen spheres which mimics native extracellular matrix, stabilizes the ventricular geometry for dynamic culture conditions, and provides a means for incorporating vascular cells for neurovascular development. Finally, we demonstrate that human organoids grown under these conditions exhibit dramatically enlarged ventricles and delayed maturation compared to mouse. Together, this approach provides a model of the forebrain neuroepithelium with morphogenetic macroscale geometry and tissue architecture, suitable for investigating neurodevelopment and disease.

ADGRL4 is an adhesion G protein-coupled receptor (aGPCR) implicated in tumour progression in multiple malignancies. We recently determined the first cryo-EM structure of active-state ADGRL4, revealing its weak coupling to the heterotrimeric G protein Gq and providing insights into its activation mechanism. Here, we describe a complete modular workflow for purifying active-state ADGRL4 over 2–3 days using a multifunctional tagging strategy incorporating multiple orthogonal detection, purification, and cleavage tags at the N-terminus as well as a tethered mini-Gq at the C-terminus. This configuration enhanced receptor cell-surface expression and stability and allowed different purification strategies to be tested during the development of the purification protocol. Although developed and optimised for ADGRL4, this approach is readily transferable to other weakly coupling aGPCRs or GPCRs where complex stability is a limiting factor for structural analysis.Key features• Complete workflow for purifying active-state ADGRL4 for cryo-EM analysis.• Modular, multifunctional N-terminal tagging strategy supporting multiple orthogonal purification and detection methods without any negative effect on cell surface expression levels.• Tethered mini-Gq increases stability and receptor cell-surface expression.• Modular purification tagging configuration provides freedom to change purification methodologies without having to perform additional receptor engineering or cloning.

DNA polymerases are complex molecular machines capable of replicating genetic material using a template-driven process. While the copying function of these enzymes is well established, their ability to perform untemplated DNA synthesis is less well characterized. Here, we explore the ability of DNA polymerases to synthesize DNA fragments in the absence of a template. We use long-read nanopore sequencing, real-time fluorescence assays, and atomic force microscopy to observe the synthesis and physical structure of pools of DNA products derived from a diverse set of natural and engineered DNA polymerases across varying temperatures and buffer compositions. We detail the features of the DNA fragments generated, enrichment of select sequence motifs, and demonstrate that the sequence composition of the synthesized DNA can be altered by modifying environmental conditions. This work provides extensive data to better discern the process of untemplated DNA polymerase activity and may support its potential repurposing as a technology for the guided synthesis of DNA sequences on the kilobase-scale and beyond.

Malignant pleural mesothelioma (MpM) is a lethal tumour closely linked to asbestos exposure and is a cancer of unmet clinical need with no known oncogenic drivers. Recent advancements in technologies to identify RNA-binding proteins (RBPs) has uncovered an emerging role for RBP-RNA interactions in cancer progression and we therefore assessed changes in the RBPome of patient-derived MpM cell lines. We identify over 350 RBPs showing altered RNA binding, with functions consistent with key cancer hallmarks, and we identified YBX3 as a potential oncoprotein driving cell proliferation in MpM. Mechanistically we show the impact of YBX3 on cell growth is achieved through its control of the expression of the amino acid transporter SLC7A5/LAT1, with increased amino acid uptake increasing protein synthesis rates. Notably, we show the inhibition of cell growth by YBX3 deletion is recapitulated by the clinically relevant SLC7A5/LAT1 inhibitor JPH203. Finally, we demonstrate that JPH203 sensitizes MpM cells to radiotherapy, which could provide a promising therapeutic strategy for MpM.

Abstract RAB5-GTP activation of the multiprotein VPS34 complex II (VPS34-CII) is critical for endosomal sorting and maturation, phagocytosis, and receptor downregulation. RAB5-GTP activates VPS34-CII, by binding to a helical insertion in the C2 domain of VPS34 on the BECLIN1/UVRAG-containing adaptor arm of the complex. The autophagy complex, VPS34 complex I (VPS34-CI), features a unique ATG14L subunit in place of the VPS34-CII UVRAG subunit, and we found that this distorts the adaptor arm to alter the VPS34 RAB-GTPase binding pocket so that it preferentially binds RAB1-GTP. Surprisingly, our higher-resolution single-particle cryo-EM structure of VPS34-CII showed a second RAB5-GTP binding site on the VPS15 solenoid region. This site (VPS15-RAB5-site) appears to be the primordial RAB5-binding region. A mutant in the helical insertion of the C2 domain of human VPS34 that mimics the Saccharomyces cerevisiae sequence abolishes RAB5 binding to VPS34. Mutation of the VPS15-RAB5-site ortholog in S. cerevisiae VPS15 resulted in defective CPY sorting, loss of colocalization with the RAB5 ortholog Vps21, and loss of binding to Vps21 in vitro . Evolutionary expansion from one to two RAB5-orthologue binding sites may have increased membrane binding and VPS34-CII activity to adapt to more complex endocytic systems.

Adoptive cell therapy (ACT) relies on durable and functional T cells to mediate tumor clearance. Th9 cells are a metabolically fit CD4+ T cell subset with strong persistence but limited cytotoxicity. Here, we identified endomelipeptide A (EpA), a cyclic peptide isolated from Ganoderma lucidum–associated endophytic fungi, as a potent enhancer of Th9 cell differentiation. EpA promoted a cytotoxic Th9 phenotype with enhanced mitochondrial function and metabolic fitness. Mechanistically, EpA dually targeted ZAP70 and SREBP1, coupling T cell receptor signaling activation with lipid metabolism suppression. EpA-treated Th9 cells mediated robust, CD8+ T cell–dependent tumor control and enhanced the efficacy of human Th9 CAR T cell therapy in vivo. These findings establish EpA as a distinct cyclic peptide that reprograms Th9 cells and provides a potential approach to boost ACT efficacy.

Abstract Perforin-2 is a pore-forming protein localised to the endocytic compartments of dendritic cells and macrophages. It is reported to perform two distinct functions during immune responses: attacking intravacuolar pathogens, and forming pores in endocytic compartments to enable cytosolic delivery of antigens during cross-presentation. The molecular mechanisms that regulate perforin-2 remain unknown. Here, we set out to address how cross-presenting dendritic cells control pore formation in phagosomes while maintaining the integrity of their endocytic compartments. We demonstrate that perforin-2 undergoes extensive proteolytic processing involving multiple endocytic proteases. Although the transmembrane anchor has been proposed to protect host membranes by orienting pores towards bacterial targets, we find that endocytic escape is mediated by full-length, membrane-anchored perforin-2 rather than by the proteolytically released ectodomain. Moreover, we show that perforin-2-mediated antigen translocation does not require low pH, explaining how perforin-2 mediated antigen import into the cytosol can occur in cross-presenting dendritic cells which do not acidify their phagosomes. Our findings point at a critical role of the transmembrane anchor in perforin-2 in dendritic cells, and reveal that pore formation occurs with striking spatiotemporal precision to safeguard the integrity of endocytic compartments.

Loss of dopamine neurons in Parkinson disease (PD) leads to motor deficits. Dopamine D2 receptor (D2R) agonists treat PD-associated motor deficits by acting on postsynaptic receptors located within the striatum that have been upregulated due dopamine loss. However, mechanisms that contribute to increased D2R activity in PD to enhance D2R function are poorly described. Spinophilin is a protein phosphatase 1 targeting protein that is expressed in postsynaptic dendritic spines and interacts with postsynaptic D2Rs. However, how spinophilin regulates D2R function is unknown. In the current study, we found that loss of spinophilin, specifically in indirect pathway medium spiny neurons and cholinergic interneurons limited the suppression of locomotion caused by the D2R agonist, quinpirole. Mechanistically, using proximity labeling in neuro2A cells and co-immunoprecipitaitons in striatal lysates from wildtype and spinophilin knockout mice, we found that spinophilin promotes the interaction of the D2R with intracellular proteins, suggesting spinophilin mediates agonist-induced D2R internalization. Therefore, our data support future studies targeting the spinophilin/D2R interaction to enhance D2R agonist activity, which may promote the efficacy of current PD therapeutics.